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Figure 1.
Fig. 1. Structure and dynamics of the SD helix. (a) (Upper)
Nucleotide sequences and base pairing between mRNA and 16S rRNA
in the initiation-like 70S ribosome complex. SD sequence,
initiator codon, and anti-SD sequences are shown in bold; shaded
nucleotides are disordered in the refined x-ray structure.
(Lower) Stereoview of the fit of the SD helix to a composite
omit density map calculated with  [A]-weighted (2F[o] –
F[c]) coefficients contoured at 1.2 . (b) Stereoview of the
nonintersecting screw axes (blue) for the SD helix (yellow). The
length of each axis is proportional to its respective
mean-square displacement value. The primary screw axis is
indicated by a rotational arrow. (c) Thermal ellipsoid
representation of the librational motions of the SD helix around
the dominant screw axis coinciding with the SD helical axis.
Atomic displacement parameters for the SD helix calculated from
the TLS model are colored according to the magnitude of the
displacements, increasing from blue (smallest) to red (largest).
The view is from the upstream end of the helix.
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